Introduction to Phylogenetic Analysis Flashcards

1
Q

the evolution of a genetically related group of organisms

A

phylogeny

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
2
Q

a study of relationships between collection of “things” (genes, proteins, organs..) that are derived from a common ancestor.

A

phylogeny

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
3
Q

the science of classification of organisms.

A

taxonomy

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
4
Q

purpose of phylogenetic tree

A
  • Find evolutionary ties between organisms. (Analyze changes occurring in different organisms during evolution).
  • Find (understand) relationships between an ancestral sequence and its descendants. (Evolution of a family of sequences)
  • Estimate the time of divergence between a group of organisms that share a common ancestor.
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
5
Q

similar sequences, ____ and this means ___

A

common ancestor; similar function

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
6
Q

From a ____ sequence, ____ are diverged. Each of these two sequences start to accumulate ____ . The number of these mutations are used in ____.

A

common ancestor; two DNA sequences; nucleotide substitutions; molecular evolution analysis

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
7
Q

How we calculate the Degree of Divergence

A

If two sequences of length N differ from
each other at n sites, then their degree of
divergence is:
n/N or n/N*100%.

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
8
Q

When 2 sequences found in 2 organisms are
very similar, we assume that they have derived
from ___

A

one ancestor

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
9
Q

The progressive multiple alignment of a group of
sequences, first aligns the ___. Then it adds the ___.

A

most similar pair; more distant pairs

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
10
Q

Most phylogenetic methods assume that each
position in a sequence can ___ from the other positions

A

change independently

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
11
Q

Gaps in alignments represent mutations in
sequences such as:

A

insertion, deletion, genetic rearrangments

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
12
Q

Gaps are treated in various ways by thephylogenetic methods. Most of them ___.

A

ignore gaps

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
13
Q

Another approach to treat gaps is by using ____ as the base for the phylogenetic analysis, instead of using the ___, and trying to decide what happened at each position.

A

sequences similarity scores; alignment itself

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
14
Q

The similarity scores based on scoring matrices (with gaps scores) are used by
the ___

A

DISTANCE methods

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
15
Q

what is a phylogenetic tree?

A

An illustration of the evolutionary relationships among a group of organisms.

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
16
Q

another name for a phylogenetic tree.

A

dendrogram

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
17
Q

A tree is composed of ___ and ___. One branch connects any two adjacent nodes. ___represent the taxonomic units. (____)

A

nodes and branches; Nodes; sequences

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
18
Q

very similar sequences will be neighbors on the outer branches and will be connected by a ____

A

common internal branch

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
19
Q

types of trees

A

trees and networks

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
20
Q

type of tree that has only one path between
any pair of nodes

A

tree

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
21
Q

a type of tree with more than one path between any pair of
nodes

A

network

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
22
Q

Represent the taxa (sequences)

A

Leaves = Outer branches

23
Q

Represent the relationships among the taxa (sequences)

A

Nodes = 1 2 3

24
Q

The length of the branch represent the # of changes that occurred in the __ prior to the next level of separation

A

sequence (branch)

25
- are branches that end with a tip - more evident diversions
external branches
26
- are branches that do not end with a tip. - more ancient diversions
internal branches
27
In a phylogenetic tree, Each ___ represents a speciation event in evolution. Beyond this point, any sequence changes that occurred are specific for each branch (specie).
node
28
In a phylogenetic tree, The -- connects -- of the tree. The length of each -- between one -- to the next, represents the # of changes that occurred until the next separation (speciation).
BRANCH; 2 NODES; BRANCH; NODE
29
In a phylogenetic tree, note that The ____ from the separation of the 2 sequences is not known. The phylogenetic analysis can only estimate the ___
amount of evolutionary time that passed; # of changes that occurred from the time of separation
30
After the ___, one taxon (sequence) can undergo more mutations then the other taxon
branching event
31
the branching pattern of a tree
topology of a tree
32
What represents the data (e.g sequences) under comparison (A,B,C,D,E), and is also known as OTUs, (----).
terminal nodes; Operational Taxonomic Units
33
What represents inferred ancestral units (usually without empirical data), also known as HTUs, (----).
Internal nodes; Hypothetical Taxonomic Units
34
Different kinds of trees can be used to depict different aspects of evolutionary history. What are those?
1. cladogram 2. additive trees 3. ultrametric trees
35
A kind of tree that simply shows relative recency of common ancestry
cladogram
36
a cladogram with branch lengths, also called phylograms and metric trees
additive tree
37
(dendograms) special kind of additive tree in which the tips of the trees are all equidistant from the root
ultrametric tree
38
what hypothesis is this? All the mutations occur at the same rate in all the tree branches. The rate of the mutations is the same for all positions along the sequence
The Molecular Clock Hypothesis
39
What hypothesis is most suitable for closely related species?
The Molecular Clock Hypothesis
40
rooted tree = -- unrooted tree = --
cladogram; phenogram
41
- A phylogenetic tree that all the "objects" on it share a known common ancestor (the root). - There exists a particular root node - The paths from the root to the nodes correspond to evolutionary time.
Rooted Tree = Cladogram
42
- A phylogenetic tree where all the "objects" on it are related descendants - but there is not enough information to specify the common ancestor (root). - The path between nodes of the tree do not specify an evolutionary time.
Unrooted Tree = Phenogram
43
The number of tree topologies of rooted tree is ___ than that of the unrooted tree for the same umber of OTUs. Therefore, the error of the unrooted tree topology is ____ than that of the rooted tree.
much higher; smaller
44
genes related by speciation events. Meaning same genes in different species.
orthologs
45
genes related by duplication events. Meaning duplicated genes in the same species.
paralogs
46
The rate of mutation is assumed to be the same in both coding and non-coding regions. However, there is a difference in the ___ .
substitution rate
47
___ have more substitution than coding regions. ____ are much more conserved since they "need" to conserve their function.
Non-coding DNA regions; Proteins
48
it is better to use sequences that mutate slowly. This is ----. However, if the genes are very small, or they mutate slowly, we can use them for ---.
protiens; building the trees
49
Are treated differently by different alignment programs and should play no part in building trees.
gaps
50
Alignment of a coding region should be compared with the alignment of their ____, to be sure about the placement of gaps.
protein sequences
51
effect the multiple alignment because they create random bias for various regions of the alignment - should be removed from the alignment before building the tree
Low complexity regions
52
If you delete low complexity regions, you need to consider the effect of the ___ on the branch lengths of the whole tree.
deletions
53
Sequences that are being compared belong together (----).
orthologs
54
If no ancestral sequence is available you may use an "___" as a reference to measure distances. In such a case, for an ---- you need to choose a close relative to the group being compared.
outgroup; outgroup